Package: Metab

Version: 1.16.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Metab.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Metab_1.16.1.tar.gz

StartedAt: 2019-04-16 01:07:21 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:10:20 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 179.3 seconds

RetCode: 0

Status:  OK

CheckDir: Metab.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Metab.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Metab_1.16.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/Metab.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Metab/DESCRIPTION’ ... OK
* this is package ‘Metab’ version ‘1.16.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Metab’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
MetReport: no visible global function definition for ‘read.csv’
MetReport: no visible global function definition for ‘write.csv’
MetReportNames: no visible global function definition for ‘read.csv’
MetReportNames: no visible global function definition for ‘write.csv’
buildLib: no visible global function definition for ‘read.csv’
buildLib: no visible global function definition for ‘txtProgressBar’
buildLib: no visible global function definition for ‘setTxtProgressBar’
buildLib: no visible global function definition for ‘write.csv’
htest : test.t : <anonymous>: no visible global function definition for
  ‘t.test’
htest : anova.t : <anonymous>: no visible global function definition
  for ‘lm’
htest : anova.t: no visible binding for global variable ‘anova’
htest: no visible global function definition for ‘read.csv’
htest: no visible global function definition for ‘p.adjust’
htest: no visible global function definition for ‘write.csv’
normalizeByBiomass: no visible global function definition for
  ‘read.csv’
normalizeByBiomass: no visible global function definition for
  ‘write.csv’
normalizeByInternalStandard: no visible global function definition for
  ‘read.csv’
normalizeByInternalStandard: no visible global function definition for
  ‘select.list’
normalizeByInternalStandard: no visible global function definition for
  ‘write.csv’
removeFalsePositives: no visible global function definition for
  ‘read.csv’
removeFalsePositives: no visible global function definition for
  ‘write.csv’
Undefined global functions or variables:
  anova lm p.adjust read.csv select.list setTxtProgressBar t.test
  txtProgressBar write.csv
Consider adding
  importFrom("stats", "anova", "lm", "p.adjust", "t.test")
  importFrom("utils", "read.csv", "select.list", "setTxtProgressBar",
             "txtProgressBar", "write.csv")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/Metab.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Metab
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘Metab’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Metab)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("Metab")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


This is MSnbase version 2.8.3 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:stats':

    smooth

The following object is masked from 'package:base':

    trimws


This is xcms version 3.4.4 


Attaching package: 'xcms'

The following object is masked from 'package:stats':

    sigma

AMDIS Report - Data frame loaded...
File 1 (130513_REF_SOL2_2_50_50_1.CDF) done!
AmdisReport - Data frame loaded...
File 130513_REF_SOL2_2_100_1 done!
Data frame loaded...
Biomass loaded...
Data frame loaded...
Data frame loaded...


RUNIT TEST PROTOCOL -- Tue Apr 16 01:10:15 2019 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Metab RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  8.158   0.490   8.697 

name	user	system	elapsed
MetReport	0.097	0.031	0.160
MetReportNames	0.095	0.003	0.100
Metab-package	0.005	0.002	0.007
buildLib	1.267	0.028	1.307
exampleAMDISReport	0.084	0.026	0.111
exampleBiomass	0.001	0.001	0.003
exampleHtest	0.002	0.001	0.003
exampleIonLib	0.006	0.002	0.009
exampleMSLfile	0.015	0.003	0.017
exampleMetReport	0.003	0.002	0.005
htest	0.109	0.017	0.129
normalizeByBiomass	0.017	0.004	0.021
normalizeByInternalStandard	0.010	0.003	0.013
removeFalsePositives	0.026	0.005	0.030